2YOB.A | AGXT – ASTRID

2YOB.A | AGXT

General Structure Information

PDB ID	2yob
HGNC Gene Label(s)	AGXT
Structure Name	high resolution agxt_m structure
Resolution	1.9Å
Reference	AUTH N.MESA-TORRES,I.FABELO-ROSA,D.RIVEROL,C.YUNTA,A.ALBERT,AUTH 2 E.SALIDO,A.L.PEYTITL THE ROLE OF PROTEIN DENATURATION ENERGETICS AND MOLECULARTITL 2 CHAPERONES IN THE AGGREGATION AND MISTARGETING OF MUTANTSTITL 3 CAUSING PRIMARY HYPEROXALURIA TYPE IREF PLOS ONE V. 8 71963 2013REFN ISSN 1932-6203PMID 24205397DOI 10.1371/JOURNAL.PONE.0071963

Variant Set Distributions

ExAC Variants

Number Of Residues	385
Number Of SNVs	127
Number Of Permutations	64030
Optimal Distance Threshold	18.0
K Statistic	0.201
p-value	0.187

ClinVar

Number Of Residues	385
Number Of SNVs	75
Number Of Permutations	45024
Optimal Distance Threshold	23.0
K Statistic	0.486
p-value	0.0

COSMIC

Number Of Residues	385
Number Of SNVs	11
Number Of Permutations	8698
Optimal Distance Threshold	25.0
K Statistic	0.527
p-value	0.756

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	127
Number Of ClinVar SNVs	72
Optimal Distance Threshold	17.0
K Statistic	0.086
p-value	0.001

Cosmic vs. ExAC

Number Of ExAC SNVs	127
Number Of COSMIC SNVs	10
Optimal Distance Threshold	26.0
K Statistic	0.255
p-value	0.131

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:241808293		H>L	A:4	(11.79, 4.56, -65.28)
2:241808308	rs115014558	T>N	A:9	(11.93, 0.14, -52.30)
2:241808311		P>H	A:10	(8.71, -1.72, -51.82)
2:241808317	rs142969817	K>R	A:12	(10.42, -5.50, -46.43)
2:241808323	rs552120667	L>R	A:14	(3.64, -2.29, -45.51)
2:241808325		L>I	A:15	(5.06, -6.60, -47.68)
2:241808331		P>T	A:17	(0.38, -8.96, -41.70)
2:241808332		P>L	A:17	(0.38, -8.96, -41.70)
2:241808347	rs34885252	N>S	A:22	(-5.78, -7.88, -27.76)
2:241808352		L>I	A:24	(-8.65, -3.26, -21.23)
2:241808356	rs180177262 COSM477175 CM072846	L>R	A:25	(-8.20, 0.81, -23.47)
2:241808362		G>V	A:27	(-7.96, 5.37, -19.68)
2:241808364	rs376684240	P>S	A:28	(-8.02, 8.90, -20.38)
2:241808382		P>S	A:34	(-18.70, -1.25, -28.95)
2:241808386		P>L	A:35	(-19.87, -4.67, -30.95)
2:241808388	rs180177157 CM072851	R>C	A:36	(-24.48, -1.09, -32.79)
2:241808389	rs180177162 CM093784	R>H	A:36	(-24.48, -1.09, -32.79)
2:241808395		M>R	A:38	(-16.18, -2.94, -34.25)
2:241808403	rs121908523	G>R	A:41	(-16.42, 0.39, -39.65)
2:241808406		G>R	A:42	(-16.83, -2.11, -41.96)
2:241808407	rs180177170 CM093785	G>E	A:42	(-16.83, -2.11, -41.96)
2:241808410		L>Q	A:43	(-19.79, -0.71, -43.39)
2:241808419		I>T	A:46	(-21.96, 6.13, -49.09)
2:241808421	rs180177173 COSM3910014 CM072843	G>R	A:47	(-21.64, 9.19, -50.93)
2:241808427	rs74205173	M>L	A:49	(-22.37, 15.28, -51.58)
2:241808588	rs180177180 CM093786	I>N	A:56	(-26.44, 9.48, -41.78)
2:241808593		D>N	A:58	(-29.72, 15.05, -40.60)
2:241808596	COSM3579992	E>K	A:59	(-29.99, 10.37, -38.03)
2:241808606		E>A	A:62	(-31.55, 14.39, -34.45)
2:241808609		G>D	A:63	(-27.81, 13.42, -31.11)
2:241808620		V>M	A:67	(-25.94, 14.36, -25.90)
2:241808635		N>H	A:72	(-28.77, 25.06, -30.69)
2:241808644		T>A	A:75	(-25.41, 21.46, -34.17)
2:241808666	rs121908522	G>E	A:82	(-11.00, 17.86, -29.99)
2:241808686	rs369184209	A>T	A:89	(-14.47, 27.88, -31.57)
2:241808687	rs200654123	A>V	A:89	(-14.47, 27.88, -31.57)
2:241808698		V>M	A:93	(-15.78, 33.39, -31.61)
2:241808705		E>V	A:95	(-12.16, 39.26, -34.32)
2:241808717	rs180177192	S>Y	A:99	(-11.05, 39.57, -24.42)
2:241808723	rs180177195 CM093792	L>P	A:101	(-11.46, 34.79, -19.35)
2:241808735		N>S	A:105	(-7.74, 24.13, -14.28)
2:241808741		I>T	A:107	(-3.73, 20.53, -20.59)
2:241808743	rs180177197 CM983924	W>R	A:108	(-7.39, 19.82, -21.99)
2:241808758		V>M	A:113	(-3.95, 30.05, -23.79)
2:241808761		D>Y	A:114	(-1.48, 28.07, -27.43)
2:241808768		G>V	A:116	(-5.52, 32.44, -28.70)
2:241808779		G>R	A:120	(-4.94, 37.34, -31.44)
2:241810073	rs180177211	H>P	A:124	(-6.94, 37.90, -20.17)
2:241810796	rs121908524	F>I	A:152	(-12.11, 27.45, -21.73)
2:241810797		F>S	A:152	(-12.11, 27.45, -21.73)
2:241810808	rs121908530	G>R	A:156	(-13.78, 17.82, -17.65)
2:241810823		G>S	A:161	(-10.19, 14.89, -12.10)
2:241810826	rs147497484	V>M	A:162	(-11.73, 18.13, -11.78)
2:241810833	rs528938116	Q>L	A:164	(-16.15, 23.05, -13.00)
2:241810838	rs543832032	L>I	A:166	(-21.36, 24.23, -15.30)
2:241810844		G>S	A:168	(-24.41, 30.12, -13.37)
2:241810850	rs121908529	G>R	A:170	(-23.96, 31.77, -17.94)
2:241810862		H>N	A:174	(-24.96, 35.63, -20.78)
2:241810865		R>W	A:175	(-24.91, 39.26, -15.19)
2:241812422	rs536205988 COSM1176489	S>L	A:184	(-17.56, 18.17, -22.90)
2:241812428	rs117195882	A>V	A:186	(-14.65, 14.02, -20.58)
2:241812431	rs180177238 CM920012	S>F	A:187	(-18.11, 15.12, -19.47)
2:241812439	rs180177239 COSM574425 CM993607	G>R	A:190	(-20.99, 10.92, -17.40)
2:241812451		Y>N	A:194	(-28.41, 19.73, -17.94)
2:241812454	rs180177243 CM093800	M>V	A:195	(-26.08, 23.79, -24.00)
2:241812460	rs556062091	R>W	A:197	(-30.65, 23.90, -16.99)
2:241812461	rs34664134	R>Q	A:197	(-30.65, 23.90, -16.99)
2:241813402	rs180177246 CM056519	D>E	A:201	(-23.09, 30.19, -25.66)
2:241813413	rs180177248 CM093803 CM093802	S>L	A:205	(-17.19, 16.70, -27.33)
2:241813421		Q>K	A:208	(-12.31, 9.71, -28.09)
2:241813422		Q>R	A:208	(-12.31, 9.71, -28.09)
2:241813434		N>S	A:212	(-17.44, 4.23, -26.75)
2:241813437	rs569680503 COSM1018788	A>V	A:213	(-16.03, 6.24, -30.74)
2:241813445	rs180177252 CM065967	G>R	A:216	(-11.61, 12.12, -35.18)
2:241813446		G>E	A:216	(-11.61, 12.12, -35.18)
2:241813475		A>S	A:226	(-22.54, 32.78, -31.01)
2:241813478		K>E	A:227	(-25.22, 32.65, -35.47)
2:241814528		K>M	A:228	(-24.58, 38.08, -34.10)
2:241814532		K>N	A:229	(-19.15, 37.37, -32.59)
2:241814534		M>T	A:230	(-19.58, 33.30, -35.60)
2:241814542	rs121908526	R>C	A:233	(-15.40, 37.67, -37.73)
2:241814546	rs202155784	K>R	A:234	(-15.67, 43.68, -40.07)
2:241814549		T>M	A:235	(-12.31, 39.39, -39.98)
2:241814554	rs370089156	P>A	A:237	(-11.93, 33.09, -40.27)
2:241814555	rs374029419	P>L	A:237	(-11.93, 33.09, -40.27)
2:241814563		F>I	A:240	(-11.78, 26.92, -46.06)
2:241814566		Y>H	A:241	(-10.91, 21.60, -42.38)
2:241814573		D>G	A:243	(-15.44, 28.70, -41.98)
2:241814575		I>V	A:244	(-18.87, 27.96, -38.99)
2:241814576	rs121908525	I>T	A:244	(-18.87, 27.96, -38.99)
2:241814585		L>R	A:247	(-18.84, 23.60, -41.66)
2:241814587	rs180177260	A>S	A:248	(-23.21, 25.25, -41.59)
2:241814588	rs372482918	A>V	A:248	(-23.21, 25.25, -41.59)
2:241814596		W>R	A:251	(-22.85, 18.69, -41.04)
2:241814602	rs180177264 CM056288	C>R	A:253	(-27.54, 24.63, -40.51)
2:241814603		C>S	A:253	(-27.54, 24.63, -40.51)
2:241814608	rs547633289	D>N	A:255	(-31.51, 29.10, -45.81)
2:241814615		P>H	A:257	(-28.44, 24.83, -50.89)
2:241814619		R>S	A:258	(-26.48, 20.24, -47.72)
2:241815356		H>Y	A:261	(-15.80, 22.72, -47.03)
2:241815368		P>S	A:265	(-15.61, 11.53, -42.16)
2:241815371	rs142114432	V>I	A:266	(-18.34, 8.50, -44.52)
2:241815372		V>A	A:266	(-18.34, 8.50, -44.52)
2:241815384	rs376364034	Y>C	A:270	(-21.16, 4.81, -41.66)
2:241815397	rs146525143	E>D	A:274	(-24.46, 3.16, -34.38)
2:241815399		S>I	A:275	(-22.44, 6.23, -30.62)
2:241815411	rs140992177	I>T	A:279	(-26.34, 7.17, -25.33)
2:241815413		A>S	A:280	(-30.35, 6.86, -26.93)
2:241816972	rs180177290 CM993608	R>C	A:289	(-27.69, 5.36, -12.62)
2:241816973	rs61729604	R>H	A:289	(-27.69, 5.36, -12.62)
2:241816984		E>K	A:293	(-22.94, 3.09, -9.80)
2:241816990	rs13408961	A>T	A:295	(-16.50, 5.58, -9.62)
2:241817016		Q>H	A:303	(-9.21, 4.68, -0.79)
2:241817038	rs369821955	V>M	A:311	(-9.75, 14.94, -6.00)
2:241817048	rs138582006	P>L	A:314	(-16.05, 13.60, -3.37)
2:241817439		A>T	A:315	(-18.04, 16.52, -5.45)
2:241817440	rs574507041	A>V	A:315	(-18.04, 16.52, -5.45)
2:241817445		R>W	A:317	(-13.85, 12.68, -6.59)
2:241817469		A>T	A:325	(-1.54, 9.76, -6.10)
2:241817472	rs115057148	V>I	A:326	(2.21, 8.82, -7.26)
2:241817478	rs200819267	A>T	A:328	(5.82, 7.15, -2.13)
2:241817481		G>S	A:329	(8.60, 5.03, -3.77)
2:241817496		D>N	A:334	(7.79, 0.84, -13.53)
2:241817497		D>G	A:334	(7.79, 0.84, -13.53)
2:241817502	COSM215866	V>I	A:336	(2.03, 2.06, -16.44)
2:241817509		Y>F	A:338	(3.41, -5.31, -13.56)
2:241817511		V>I	A:339	(-0.68, -2.84, -15.84)
2:241817515		I>T	A:340	(0.11, -3.39, -20.72)
2:241817516	rs4426527	I>M	A:340	(0.11, -3.39, -20.72)
2:241817519	rs144007007	D>E	A:341	(3.75, -5.80, -19.54)
2:241817526	rs372399525	D>N	A:344	(-3.00, -6.94, -21.51)
2:241817529	rs372799517	I>F	A:345	(-4.71, -3.08, -18.52)
2:241817532		E>K	A:346	(-4.15, 1.95, -21.36)
2:241817538		M>V	A:348	(-2.09, 7.00, -18.76)
2:241817544	rs199610919	G>S	A:350	(-0.09, 12.51, -16.62)
2:241818137		R>W	A:360	(-4.73, 9.99, -16.36)
2:241818143	rs569643246	G>S	A:362	(-10.94, 5.14, -16.97)
2:241818167	rs372138644	R>C	A:370	(-18.72, -3.44, -9.88)
2:241818168		R>H	A:370	(-18.72, -3.44, -9.88)
2:241818170	rs369664123	E>K	A:371	(-15.46, -6.76, -15.46)
2:241818182	rs552474817	R>C	A:375	(-10.36, -7.42, -15.13)
2:241818183		R>H	A:375	(-10.36, -7.42, -15.13)
2:241818185		V>M	A:376	(-7.61, -1.84, -12.85)
2:241818189		T>M	A:377	(-7.76, -3.00, -8.75)
2:241818201	rs151185188	R>K	A:381	(-3.73, -6.36, -5.92)
2:241818203	rs534914463	A>T	A:382	(0.47, -6.54, -8.62)

[+] ClinVar Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:241808304	rs796052057	V>L	A:8	(11.66, 4.25, -52.66)
2:241808310	rs180177191	P>T	A:10	(8.71, -1.72, -51.82)
2:241808356	rs180177262	L>R	A:25	(-8.20, 0.81, -23.47)
2:241808359	rs180177268	L>P	A:26	(-8.99, 1.18, -18.33)
2:241808388	rs180177157	R>C	A:36	(-24.48, -1.09, -32.79)
2:241808389	rs180177162	R>H	A:36	(-24.48, -1.09, -32.79)
2:241808403	rs121908523	G>R	A:41	(-16.42, 0.39, -39.65)
2:241808404	rs180177168	G>E	A:41	(-16.42, 0.39, -39.65)
2:241808407	rs180177170	G>E	A:42	(-16.83, -2.11, -41.96)
2:241808421	rs180177173	G>R	A:47	(-21.64, 9.19, -50.93)
2:241808588	rs180177180	I>N	A:56	(-26.44, 9.48, -41.78)
2:241808596	rs767586362	E>K	A:59	(-29.99, 10.37, -38.03)
2:241808608	rs180177181	G>R	A:63	(-27.81, 13.42, -31.11)
2:241808630	rs796052058	T>N	A:70	(-29.60, 21.65, -27.67)
2:241808663	rs180177184	S>L	A:81	(-9.94, 15.98, -32.75)
2:241808665	rs180177185	G>R	A:82	(-11.00, 17.86, -29.99)
2:241808666	rs121908522	G>E	A:82	(-11.00, 17.86, -29.99)
2:241808669	rs180177186	H>R	A:83	(-7.06, 19.66, -29.54)
2:241808675	rs796052059	A>D	A:85	(-13.38, 21.76, -31.78)
2:241808704	rs180177189	E>K	A:95	(-12.16, 39.26, -34.32)
2:241808723	rs180177195	L>P	A:101	(-11.46, 34.79, -19.35)
2:241808729	rs180177196	G>E	A:103	(-9.50, 28.30, -17.25)
2:241808743	rs180177197	W>R	A:108	(-7.39, 19.82, -21.99)
2:241808745	rs796052060	W>C	A:108	(-7.39, 19.82, -21.99)
2:241808747	rs180177199	G>V	A:109	(-6.57, 25.74, -20.79)
2:241808753	rs180177203	R>Q	A:111	(-3.27, 22.55, -25.38)
2:241808756	rs796052061	A>D	A:112	(-6.86, 27.71, -24.93)
2:241808767	rs180177207	G>R	A:116	(-5.52, 32.44, -28.70)
2:241808773	rs376844297	R>S	A:118	(-0.83, 29.83, -32.20)
2:241808774	rs138025751	R>H	A:118	(-0.83, 29.83, -32.20)
2:241810073	rs180177211	H>P	A:124	(-6.94, 37.90, -20.17)
2:241810125	rs180177217	E>D	A:141	(-12.49, 38.73, -9.85)
2:241810791	rs180177222	L>P	A:150	(-15.07, 33.93, -24.86)
2:241810796	rs121908524	F>I	A:152	(-12.11, 27.45, -21.73)
2:241810799	rs180177223	L>V	A:153	(-14.91, 26.89, -18.25)
2:241810808	rs121908530	G>R	A:156	(-13.78, 17.82, -17.65)
2:241810823	rs180177227	G>S	A:161	(-10.19, 14.89, -12.10)
2:241810839	rs180177230	L>H	A:166	(-21.36, 24.23, -15.30)
2:241810850	rs121908529	G>R	A:170	(-23.96, 31.77, -17.94)
2:241810860	rs180177231	C>Y	A:173	(-21.22, 35.43, -18.66)
2:241812404	rs180177235	C>Y	A:178	(-19.69, 36.83, -22.03)
2:241812418	rs180177236	D>N	A:183	(-14.23, 20.99, -22.63)
2:241812427	rs180177237	ASL>DRL	A:186	(-14.65, 14.02, -20.58)
2:241812431	rs180177238	S>F	A:187	(-18.11, 15.12, -19.47)
2:241812439	rs180177239	G>R	A:190	(-20.99, 10.92, -17.40)
2:241812454	rs180177243	M>L	A:195	(-26.08, 23.79, -24.00)
2:241812455	rs180177244	M>R	A:195	(-26.08, 23.79, -24.00)
2:241812466	rs796052062	G>S	A:199	(-26.14, 28.91, -20.85)
2:241813402	rs180177246	D>E	A:201	(-23.09, 30.19, -25.66)
2:241813404	rs536352238	I>T	A:202	(-19.71, 27.49, -27.33)
2:241813412	rs121908520	S>P	A:205	(-17.19, 16.70, -27.33)
2:241813427	rs180177250	A>P	A:210	(-18.19, 8.04, -23.37)
2:241813445	rs180177252	G>R	A:216	(-11.61, 12.12, -35.18)
2:241813452	rs180177253	S>L	A:218	(-15.82, 16.52, -32.94)
2:241813460	rs180177254	S>P	A:221	(-23.15, 23.72, -30.30)
2:241814542	rs121908526	R>C	A:233	(-15.40, 37.67, -37.73)
2:241814543	rs121908527	R>H	A:233	(-15.40, 37.67, -37.73)
2:241814572	rs180177258	D>H	A:243	(-15.44, 28.70, -41.98)
2:241814576	rs121908525	I>T	A:244	(-18.87, 27.96, -38.99)
2:241814587	rs180177260	A>S	A:248	(-23.21, 25.25, -41.59)
2:241814595	rs796052072	FW>FK	A:250	(-22.06, 19.79, -46.11)
2:241814602	rs180177264	C>R	A:253	(-27.54, 24.63, -40.51)
2:241815358	rs180177269	H>Q	A:261	(-15.80, 22.72, -47.03)
2:241815381	rs180177271	L>P	A:269	(-19.99, 9.91, -39.71)
2:241815397	rs146525143	E>D	A:274	(-24.46, 3.16, -34.38)
2:241815398	rs180177272	S>R	A:275	(-22.44, 6.23, -30.62)
2:241815405	rs796052073	A>D	A:277	(-27.72, 5.07, -30.71)
2:241815421	rs180177284	Q>H	A:282	(-28.27, 3.90, -21.70)
2:241816958	rs180177287	L>P	A:284	(-28.31, 10.99, -20.77)
2:241816966	rs180177289	S>T	A:287	(-25.12, 7.00, -18.41)
2:241816973	rs61729604	R>H	A:289	(-27.69, 5.36, -12.62)
2:241817000	rs180177293	L>P	A:298	(-12.40, 2.96, -8.69)
2:241817443	rs796052063	L>P	A:316	(-14.89, 18.35, -7.02)
2:241817452	rs180177299	P>L	A:319	(-16.76, 10.32, -13.00)
2:241817503	rs180177155	V>D	A:336	(2.03, 2.06, -16.44)
2:241817516	rs4426527	I>M	A:340	(0.11, -3.39, -20.72)
2:241817541	rs796052065	G>S	A:349	(-0.52, 9.36, -16.30)
2:241817545	rs180177156	G>D	A:350	(-0.09, 12.51, -16.62)
2:241818135	rs180177160	L>P	A:359	(-1.79, 7.25, -11.82)
2:241818138	rs180177161	R>Q	A:360	(-4.73, 9.99, -16.36)
2:241818161	rs180177163	A>T	A:368	(-18.09, 1.63, -17.10)
2:241818207	rs796052066	A>D	A:383	(2.28, -3.61, -9.35)
2:241818210	rs180177165	L>P	A:384	(1.78, -1.72, -5.91)

2YOB.A | AGXT.

2YOB.A | AGXT

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] ClinVar Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:241808314	COSM3766554	P>L	A:11	(7.75, -0.95, -47.73)
2:241808371	COSM4512329	P>L	A:30	(-8.92, 6.18, -26.56)
2:241808596	COSM3579992	E>K	A:59	(-29.99, 10.37, -38.03)
2:241812406	COSM1531648	L>M	A:179	(-19.94, 34.26, -25.22)
2:241812428	COSM249180	A>V	A:186	(-14.65, 14.02, -20.58)
2:241812439	COSM574425	G>R	A:190	(-20.99, 10.92, -17.40)
2:241815414	COSM4985251	A>V	A:280	(-30.35, 6.86, -26.93)
2:241816988	COSM1182250	A>V	A:294	(-18.12, 2.90, -11.20)
2:241817502	COSM215866	V>I	A:336	(2.03, 2.06, -16.44)
2:241817516	COSM4986441	I>M	A:340	(0.11, -3.39, -20.72)
2:241817554	COSM3714174	P>L	A:353	(-0.05, 20.37, -14.91)